[ck2cti] Add support for species names containing '+' and '='
This commit is contained in:
Ray Speth
parent
4107b268ce
commit
a289e6f613
3 changed files with 83 additions and 50 deletions
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@ -39,6 +39,9 @@ import numpy as np
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import re
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import itertools
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reFloat = re.compile(r'\+?\d*\.?\d+([eEdD][-+]?\d+)?$')
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reInt = re.compile(r'\+?\d+$')
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QUANTITY_UNITS = {'MOL': 'mol',
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'MOLE': 'mol',
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'MOLES': 'mol',
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@ -997,6 +1000,18 @@ class Parser(object):
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return species, thermo, composition, note
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def setupKinetics(self):
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self.valid_tokens = dict((k,'species') for k in self.speciesDict)
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self.valid_tokens.update(('(+%s)' % k, 'falloff3b: %s' % k) for k in self.speciesDict)
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self.valid_tokens['M'] = 'third-body'
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self.valid_tokens['m'] = 'third-body'
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self.valid_tokens['(+M)'] = 'falloff3b'
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self.valid_tokens['(+m)'] = 'falloff3b'
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self.valid_tokens['<=>'] = 'equal'
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self.valid_tokens['=>'] = 'equal'
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self.valid_tokens['='] = 'equal'
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self.Slen = max(map(len, self.valid_tokens))
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def readKineticsEntry(self, entry):
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"""
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Read a kinetics `entry` for a single reaction as loaded from a
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@ -1034,19 +1049,48 @@ class Parser(object):
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n = float(tokens[-2])
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Ea = float(tokens[-1])
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reaction = ''.join(tokens[:-3])
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revReaction = None
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# Split the reaction equation into reactants and products
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if '<=>' in reaction:
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reversible = True
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reactants, products = reaction.split('<=>')
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elif '=>' in reaction:
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reversible = False
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reactants, products = reaction.split('=>')
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elif '=' in reaction:
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reversible = True
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reactants, products = reaction.split('=')
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else:
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# Identify tokens comprising the reaction expression. Look for the
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# longest possible sub-sequences first.
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locs = {}
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for i in range(self.Slen, 0, -1):
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for j in range(len(reaction)-i+1):
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test = reaction[j:j+i]
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if test in self.valid_tokens:
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reaction = reaction[:j] + ' '*i + reaction[j+i:]
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locs[j] = test, self.valid_tokens[test]
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# Anything that's left should be a stoichiometric coefficient or a '+'
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# between species
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for token in reaction.split():
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j = reaction.find(token)
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i = len(token)
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reaction = reaction[:j] + ' '*i + reaction[j+i:]
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if reInt.match(token):
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locs[j] = int(token), 'coeff'
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elif reFloat.match(token):
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locs[j] = float(token), 'coeff'
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elif token != '+':
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raise InputParseError('Unexpected token "{0}" in reaction expression "{1}".'.format(token, reaction))
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reactants = []
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products = []
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stoichiometry = 1
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lhs = True
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for token,kind in [v for k,v in sorted(locs.items())]:
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if kind == 'equal':
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reversible = token in ('<=>', '=')
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lhs = False
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elif kind == 'coeff':
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stoichiometry = token
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elif lhs:
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reactants.append((stoichiometry,token,kind))
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stoichiometry = 1
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else:
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products.append((stoichiometry,token,kind))
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stoichiometry = 1
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if lhs is True:
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raise InputParseError("Failed to find reactant/product delimiter in reaction string.")
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# Create a new Reaction object for this reaction
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@ -1055,39 +1099,13 @@ class Parser(object):
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def parseExpression(expression, dest):
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falloff3b = None
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thirdBody = False # simple third body reaction (non-falloff)
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# Look for third-body species for falloff reactions
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if re.search(r'\(\+[Mm]\)', expression):
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falloff3b = 'M'
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expression = re.sub(r'(\(\+[Mm]\))', '', expression)
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elif re.search(r'\(\+.*\)', expression):
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# See if it matches a known species
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for species in self.speciesDict:
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if re.search(r'\(\+%s\)' % re.escape(species), expression):
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falloff3b = species
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expression = re.sub(r'(\(\+%s\))' % re.escape(species),
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'', expression)
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break
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for term in expression.split('+'):
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term = term.strip()
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if term[0].isdigit() or term[0] == '.':
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# This allows for for non-unity stoichiometric coefficients, e.g.
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# 2A=B+C or .85A+.15B=>C
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j = [i for i in range(len(term)) if isnumberlike(term[:i])][-1]
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if term[:j].isdigit():
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stoichiometry = int(term[:j])
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else:
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stoichiometry = float(term[:j])
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species = term[j:]
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else:
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species = term
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stoichiometry = 1
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if species == 'M' or species == 'm':
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for stoichiometry,species,kind in expression:
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if kind == 'third-body':
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thirdBody = True
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elif species not in self.speciesDict:
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raise InputParseError('Unexpected species "{0}" in reaction expression "{1}".'.format(species, expression))
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elif kind == 'falloff3b':
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falloff3b = 'M'
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elif kind.startswith('falloff3b:'):
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falloff3b = kind.split()[1]
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else:
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dest.append((stoichiometry, self.speciesDict[species]))
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@ -1116,7 +1134,6 @@ class Parser(object):
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quantity_dim + 1, quantity_units)
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# The rest of the first line contains Arrhenius parameters
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tokens = lines[0].split()[1:]
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arrhenius = Arrhenius(
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A=(A,kunits),
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n=n,
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@ -1554,6 +1571,7 @@ class Parser(object):
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if len(kineticsList) != len(commentsList):
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commentsList = ['' for kinetics in kineticsList]
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self.setupKinetics()
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for kinetics, comments, line_number in zip(kineticsList, commentsList, startLines):
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try:
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reaction,revReaction = self.readKineticsEntry(kinetics)
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@ -2,7 +2,7 @@ Elements
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H C
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End
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SPEC
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(Parens) @#$%^-2 [xy2]*{.}
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(Parens) @#$%^-2 [xy2]*{.} plus+ eq=uals
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end
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thermo
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@ -19,9 +19,20 @@ thermo
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7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13 2
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-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05 3
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-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00 4
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plus+ C 1H 4 G 200.000 3500.000 1000.000 1
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7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13 2
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-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05 3
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-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00 4
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eq=uals C 1H 4 G 200.000 3500.000 1000.000 1
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7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13 2
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-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05 3
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-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00 4
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end
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reaction
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(Parens) + @#$%^-2 = 2 [xy2]*{.} 1.2345e12 1.0 200.0
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2(Parens) + [xy2]*{.} = 3@#$%^-2 5.4321e10 1.0 500.0
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plus+ + (Parens) = 2plus+ 9.999e9 9.9 999.9
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2 plus+ + eq=uals = 3(Parens) 9.999e9 9.9 999.9
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end
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@ -119,15 +119,19 @@ class chemkinConverterTest(utilities.CanteraTest):
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outName='species-names.cti', quiet=True)
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gas = ct.IdealGasMix('species-names.cti')
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self.assertEqual(gas.nSpecies(), 3)
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self.assertEqual(gas.nSpecies(), 5)
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self.assertEqual(gas.speciesName(0), '(Parens)')
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self.assertEqual(gas.speciesName(1), '@#$%^-2')
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self.assertEqual(gas.speciesName(2), '[xy2]*{.}')
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self.assertEqual(gas.speciesName(3), 'plus+')
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self.assertEqual(gas.speciesName(4), 'eq=uals')
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self.assertEqual(gas.nReactions(), 2)
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self.assertEqual(gas.nReactions(), 4)
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nu = gas.productStoichCoeffs() - gas.reactantStoichCoeffs()
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self.assertEqual(list(nu[:,0]), [-1, -1, 2])
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self.assertEqual(list(nu[:,1]), [-2, 3, -1])
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self.assertEqual(list(nu[:,0]), [-1, -1, 2, 0, 0])
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self.assertEqual(list(nu[:,1]), [-2, 3, -1, 0, 0])
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self.assertEqual(list(nu[:,2]), [-1, 0, 0, 1, 0])
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self.assertEqual(list(nu[:,3]), [3, 0, 0, -2, -1])
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def test_unterminatedSections(self):
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self.assertRaises(ck2cti.InputParseError,
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